I just spray the inside of the tub my chosen main color (usually a flat lacquer), brush paint secondary colors, then just brush paint the portion of the tub that will be visible underneath with flat black, usually the driveshaft tunnel and the area around the firewall.
I keep forgetting to try clear enamel, but I have had some success using Future floor polish for light lenses. Don't think it's quite strong enough for glass though.
as one applies these lenses, how do you keep the lines parallel to the ground and each other?
I'll assume you mean the molded-in lines on a headlight lens? I just eyeball it as close as possible when installing them, then rotate as needed with a toothpick or tip of a hobby blade before the adhesive sets.